Publications
Zheng Y*, Caron D*, Kim J, Jun S, Tian Y, Florian M, Stuart K, Sims P, Gottardo R. ADTnorm: robust integration of single-cell protein measurement across CITE-seq datasets. Nat Commun. 2025 Jul 1;16(1):5852. doi: 10.1038/s41467-025-61023-6. PMID: 40595741; PMCID: PMC12218154.
Zheng Y, Ahmad K, Henikoff S. Total whole-arm chromosome losses predict malignancy in human cancer. Proc Natl Acad Sci U S A. 2025 May 6;122(18):e2505385122. doi: 10.1073/pnas.2505385122. Epub 2025 May 2. PMID: 40314975; PMCID: PMC12067283.
Henikoff S*, Zheng Y*, Paranal R, Xu Y, Greene J, Henikoff J, Russell Z, Szulzewsky F, Thirimanne H, Kugel S, Holland E, Ahmad K. RNA polymerase II at histone genes predicts outcome in human cancer. Science. 2025 Jan 2;387(6735):737-743. doi: 10.1126/science.ads2169. Epub 2025 Feb 13. PMID: 39946483; PMCID: PMC12184985.
Featured in Inside Precision Medicine
Fiorenza S*, Zheng Y*, Purushe J, Bock T, Sarthy J, Janssens D, Sheih A, Kimble E, Kirchmeier D, Phi T, Gauthier J, Hirayama A, Riddell S, Wu Q, Gottardo R, Maloney D, Yang J, Henikoff S, Turtle C. Histone marks identify novel transcription factors that parse CAR-T subset-of-origin, clinical potential and expansion. Nat Commun. 2024 Sep 27;15(1):8309. doi: 10.1038/s41467-024-52503-2. PMID: 39333103; PMCID: PMC11436946.
Zheng Y*, Shen S*, Keleş S. Normalization and de-noising of single-cell Hi-C data with BandNorm and scVI-3D. Genome Biol. 2022 Oct 17;23(1):222. doi: 10.1186/s13059-022-02774-z. PMID: 36253828; PMCID: PMC9575231.
Shen S, Zheng Y+, Keleş S. scGAD: single-cell gene associating domain scores for exploratory analysis of scHi-C data. Bioinformatics. 2022 Jul 11;38(14):3642-3644. doi: 10.1093/bioinformatics/btac372. PMID: 35652733; PMCID: PMC9272792.
Germanos AA, Arora S, Zheng Y, Goddard ET, Coleman IM, Ku AT, Wilkinson S, Amezquita RA, Zager M, Long A, Yang YC, Bielas J, Gottardo R, Ghajar C, Nelson P, Sowalsky A, Setty M, Hsieh A. Defining cellular population dynamics at single-cell resolution during prostate cancer progression. Elife. 2022 Dec 13;11:e79076. doi: 10.7554/eLife.79076. PMID: 36511483; PMCID: PMC9747158.
Cheng J, Clayton J, Acemel R, Zheng Y, Taylor R, Keles S, Harley J, Quail E, Gómez-Skarmeta J and Ulgiati D. Regulatory Architecture of the RCA Gene Cluster Captures an Intragenic TAD Boundary, CTCF-Mediated Chromatin Looping and a Long-Range Intergenic Enhancer. Front Immunol. 2022 Jun 13;13:901747. doi: 10.3389/fimmu.2022.901747. PMID: 35769482; PMCID: PMC9235356.
Zheng Y, Zhou P, Keleş S. FreeHi-C spike-in simulations for benchmarking differential chromatin interaction detection. Methods. 2021 May;189:3-11. doi: 10.1016/j.ymeth.2020.07.001. Epub 2020 Jul 12. PMID: 32663510; PMCID: PMC7855360.
Huang K, Wu Y, Shin J, Zheng Y, Siahpirani A, Lin Y, Ni Z, Chen J, You J, Keleş S, Wang D, Roy S, Lu Q. Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder. PLoS Genet. 2021 Feb 4;17(2):e1009309. doi: 10.1371/journal.pgen.1009309. PMID: 33539344; PMCID: PMC7888619.
Vitanza N, Biery M, Myers C, Ferguson E, Zheng Y, Girard E, Przystal J, Park G, Noll A, Pakiam F, Winter C, Morris S, Sarthy J, Cole B, Leary S, Crane C, Lieberman N, Mueller S, Nazarian J, Gottardo R, Brusniak M, Mhyre A, Olson J. Optimal therapeutic targeting by HDAC inhibition in biopsy-derived treatment-naïve diffuse midline glioma models. Neuro Oncol. 2021 Mar 25;23(3):376-386. doi: 10.1093/neuonc/noaa249. PMID: 33130903; PMCID: PMC7992886.
Wu S, Furlan S, Mihalas A, Kaya-Okur H, Feroze H, Emerson S, Zheng Y, Carson K, Cimino P, Keene C, Holland E, Sarthy J, Gottardo R, Ahmad K, Henikoff S, Patel A. Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression. Nat Biotechnol. 2021 Jul;39(7):819-824. doi: 10.1038/s41587-021-00865-z. Epub 2021 Apr 12. PMID: 33846646; PMCID: PMC8277750.
Zheng Y, Keleş S. FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation. Nat Methods. 2020 Jan;17(1):37-40. doi: 10.1038/s41592-019-0624-3. Epub 2019 Nov 11. PMID: 31712779; PMCID: PMC8136837.
Liao R*, Zheng Y*, Liu X, Zhang Y, Seim G, Tanimura N, Wilson G, Hematti P, Coon J, Fan J, Xu J, Keleş S+ and Bresnick E+. Discovering How Heme Controls Genome Function Through Heme-omics. Cell Rep. 2020 Jun 30;31(13):107832. doi: 10.1016/j.celrep.2020.107832. PMID: 32610133; PMCID: PMC7382780.
Zheng Y, Ahmad K, Henikoff K. CUTTag Data Processing and Analysis Tutorial. Protocols.io. (2020) dx.doi.org/10.17504/protocols.io.bjk2kkye. 52,354 views, 4,355 exports and 314 questions.
The ENCODE Project Consortium, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 Jul;583(7818):699-710. doi: 10.1038/s41586-020-2493-4. Epub 2020 Jul 29. Erratum in: Nature. 2022 May;605(7909):E3. doi: 10.1038/s41586-021-04226-3. PMID: 32728249; PMCID: PMC7410828.
The ENCODE Project Consortium, et al. Perspectives on ENCODE. Nature. 2020 Jul;583(7818):693-698. doi: 10.1038/s41586-020-2449-8. Epub 2020 Jul 29. Erratum in: Nature. 2022 May;605(7909):E4. doi: 10.1038/s41586-021-04213-8. PMID: 32728248; PMCID: PMC7410827.
Zheng Y, Ay F, Keleş S. Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies. Elife. 2019 Jan 31;8:e38070. doi: 10.7554/eLife.38070. PMID: 30702424; PMCID: PMC6450682.
Soukup AA, Zheng Y, Mehta C, Liu P, Hofmann I, Zhou Y, Zhang J, Choi K, Johnson KD, Keles S, Bresnick EH. Single-nucleotide human disease mutation inactivates a blood-regenerative GATA2 enhancer. J Clin Invest. 2019 Mar 1;129(3):1180-1192. doi: 10.1172/JCI122694. Epub 2019 Feb 11. PMID: 30620726; PMCID: PMC6391105.
Tanimura N, Liao R, Wilson GM, Dent MR, Cao M, Burstyn JN, Hematti P, Liu X, Zhang Y, Zheng Y, Keleş S, Xu J, Coon J, Bresnick E. GATA/Heme Multi-omics Reveals a Trace Metal-Dependent Cellular Differentiation Mechanism. Dev Cell. 2018 Sep 10;46(5):581-594.e4. doi: 10.1016/j.devcel.2018.07.022. Epub 2018 Aug 16. PMID: 30122630; PMCID: PMC6133724.
Zeng X, Li B, Welch R, Rojo C, Zheng Y, Dewey CN, Keleş S. Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. PLoS Comput Biol. 2015 Oct 20;11(10):e1004491. doi: 10.1371/journal.pcbi.1004491. PMID: 26484757; PMCID: PMC4618727.